Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017818.1 Corchorus olitorius cultivar O-4 contig17851, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20064
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:5864 original size:35 final size:34
Alignment explanation
Indices: 5818--5888 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
5808 GTAGTTTGAC
5818 AAATTCAAAAATACTTGATATATCTTTAACAAAAA
1 AAATTCAAAAATACTTGATATATCTTTAA-AAAAA
* *
5853 AAATTCAAAAATACTTTATATATCTTTTAAAAAA
1 AAATTCAAAAATACTTGATATATCTTTAAAAAAA
5887 AA
1 AA
5889 TTCCACCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (34 bp):
AAATTCAAAAATACTTGATATATCTTTAAAAAAA
Found at i:6854 original size:20 final size:22
Alignment explanation
Indices: 6831--6871 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6821 TCGAGCTTGG
6831 CTCGAA-TTTTC-CGAGTCGAA
1 CTCGAATTTTTCTCGAGTCGAA
6851 CTCGAATTTTTCTCGAGTCGA
1 CTCGAATTTTTCTCGAGTCGA
6872 GTCCGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
CTCGAATTTTTCTCGAGTCGAA
Found at i:9036 original size:6 final size:6
Alignment explanation
Indices: 9027--9071 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
9017 TCCTTGCATA
9027 TTTAAT TTTAAT TTTAAT TTTAAT TTT-AT TATT-AT TATTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T-TTAAT T-TTAAT TTT
9072 TACACTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 3 0.08
6 31 0.84
7 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:9922 original size:22 final size:22
Alignment explanation
Indices: 9897--9994 Score: 101
Period size: 22 Copynumber: 4.4 Consensus size: 22
9887 TCAATATAAA
* *
9897 GAAGCCAAGTAGTCGAC-AAGAG
1 GAAGCAAATTAGTCGACTAAG-G
* *
9919 GAAGCAAATTTGTCGACTAAAG
1 GAAGCAAATTAGTCGACTAAGG
*
9941 GAAGCAAATTTGTCGACTAAGG
1 GAAGCAAATTAGTCGACTAAGG
*
9963 GAAGCAAAATCA-TCGACTAAGG
1 GAAGC-AAATTAGTCGACTAAGG
9985 GAAGCCAAAT
1 GAAG-CAAAT
9995 CGTTGACAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
22 59 0.89
23 7 0.11
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (22 bp):
GAAGCAAATTAGTCGACTAAGG
Found at i:9956 original size:44 final size:45
Alignment explanation
Indices: 9908--9994 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
9898 AAGCCAAGTA
* **
9908 GTCGAC-AAGAGGAAGCAAATTTGTCGACTAAAGGAAG-CAAATTT
1 GTCGACTAAG-GGAAGCAAAATCATCGACTAAAGGAAGCCAAATTT
*
9952 GTCGACTAAGGGAAGCAAAATCATCGACTAAGGGAAGCCAAAT
1 GTCGACTAAGGGAAGCAAAATCATCGACTAAAGGAAGCCAAAT
9995 CGTTGACAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 29 0.78
45 8 0.22
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.17
Consensus pattern (45 bp):
GTCGACTAAGGGAAGCAAAATCATCGACTAAAGGAAGCCAAATTT
Found at i:10973 original size:17 final size:16
Alignment explanation
Indices: 10953--11006 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
10943 TTAATTTATG
10953 CTTTAATTTTCAATTTT
1 CTTTAATTTTCAA-TTT
*
10970 CTTT-ATTTT--ATGT
1 CTTTAATTTTCAATTT
10983 CTTTAATTTTCAAGTTT
1 CTTTAATTTTCAA-TTT
*
11000 CATTAAT
1 CTTTAAT
11007 AAACTATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.20
14 6 0.20
16 6 0.20
17 12 0.40
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (16 bp):
CTTTAATTTTCAATTT
Found at i:13917 original size:25 final size:22
Alignment explanation
Indices: 13861--13917 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
13851 TTCTGCTTTC
13861 TAATTAATTGTTTTCTTTAATTT
1 TAATT-ATTGTTTTCTTTAATTT
* *
13884 TCATGATTGTTTTCTTAGATAATTT
1 TAATTATTGTTTTCTT---TAATTT
13909 TAATTATTG
1 TAATTATTG
13918 GTTTGATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.41
23 3 0.11
25 13 0.48
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (22 bp):
TAATTATTGTTTTCTTTAATTT
Found at i:14162 original size:23 final size:23
Alignment explanation
Indices: 14132--14177 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
14122 GGAGTCAGCC
14132 AAGCCCTTGAAACTTGGAACCGT
1 AAGCCCTTGAAACTTGGAACCGT
14155 AAGCCCTTGAAACTTGGAACCGT
1 AAGCCCTTGAAACTTGGAACCGT
14178 GAAACATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
AAGCCCTTGAAACTTGGAACCGT
Found at i:15228 original size:21 final size:20
Alignment explanation
Indices: 15182--15243 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
15172 TAAATATCAC
* *
15182 AATTAAAAGAAAAC--AATT
1 AATTAAAAAAAAACTAAATA
* *
15200 AATCTAAAAATAAAGTAAAGTA
1 AAT-TAAAAAAAAACTAAA-TA
15222 AATTAAAAAAAAACTAAATA
1 AATTAAAAAAAAACTAAATA
15242 AA
1 AA
15244 ACACTAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 4 0.12
21 15 0.44
22 4 0.12
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
AATTAAAAAAAAACTAAATA
Done.